Showing metabocard for Glutarate semialdehyde (MMDBc0047968)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-23 23:19:37 UTC
Update Date2024-04-30 20:34:06 UTC
Metabolite IDMMDBc0047968
Metabolite Identification
Common NameGlutarate semialdehyde
DescriptionIn the lysine degradation IV pathway, glutarate semialdehyde reacts with NADP+ and H2O to produce glutarate, NADPH, and H+. In this pathway, glutarate semialdehyde is produced by the reaction between 5-aminopentanoate and 2-ketoglutarate, with L-glutamate as a byproduct. The enzyme responsible for this reaction is 5-aminovalerate aminotransferase. In the lysine degradation III pathway, glutarate semialdehyde reacts with NAD+ and H2O to produce glutarate and NADH. In this pathway, glutarate semialdehyde is produced by the reaction between 5-aminopentanoate and 2-ketoglutarate, with L-glutamate as a byproduct. The enzyme responsible for this reaction is 5-aminovalerate aminotransferase.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000556b6ab28c18>


  Mrv0541 02241203522D          

  8  7  0  0  0  0            999 V2000
   12.9073   -8.5176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6217   -8.1051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3362   -8.5176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0507   -8.1051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7651   -8.5176    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1928   -8.1051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0507   -7.2801    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1928   -7.2801    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  7  4  2  0  0  0  0
  8  6  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x0000556b6ab28c18>

HMDB0012233
     RDKit          3D
Glutarate semialdehyde
 16 15  0  0  0  0  0  0  0  0999 V2000
   -2.5555   -0.5850   -0.5779 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2334   -0.2753    0.5552 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2863    0.8300    0.7455 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1474    0.4921    0.4720 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4102    0.0174   -0.9383 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8436   -0.2676   -1.0552 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5330    0.4095   -1.8462 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4163   -1.2703   -0.2973 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6650   -0.8365    1.3743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3208    1.1505    1.8318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5795    1.7306    0.1577 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7623    1.3679    0.7592 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4875   -0.3454    1.1342 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1265   -0.9482   -1.0955 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0966    0.7541   -1.7037 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0701   -1.0626    0.4839 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  2  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  8 16  1  0
M  END
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3D SDF for #<Metabolite:0x0000556b6ab28c18>


  Mrv0541 02241203522D          

  8  7  0  0  0  0            999 V2000
   12.9073   -8.5176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6217   -8.1051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3362   -8.5176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0507   -8.1051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7651   -8.5176    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1928   -8.1051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0507   -7.2801    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1928   -7.2801    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  7  4  2  0  0  0  0
  8  6  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0047968

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)CCCC=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O3/c6-4-2-1-3-5(7)8/h4H,1-3H2,(H,7,8)

> <INCHI_KEY>
VBKPPDYGFUZOAJ-UHFFFAOYSA-N

> <FORMULA>
C5H8O3

> <MOLECULAR_WEIGHT>
116.1152

> <EXACT_MASS>
116.047344122

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
11.259526180472978

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-oxopentanoic acid

> <ALOGPS_LOGP>
-0.07

> <JCHEM_LOGP>
-0.11253055466666681

> <ALOGPS_LOGS>
-0.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.093422671780562

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.327464753861699

> <JCHEM_PKA_STRONGEST_BASIC>
-6.944627704913942

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
27.212600000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.03e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-oxopentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x0000556b6ab28c18>

HMDB0012233
     RDKit          3D
Glutarate semialdehyde
 16 15  0  0  0  0  0  0  0  0999 V2000
   -2.5555   -0.5850   -0.5779 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2334   -0.2753    0.5552 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2863    0.8300    0.7455 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1474    0.4921    0.4720 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4102    0.0174   -0.9383 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8436   -0.2676   -1.0552 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5330    0.4095   -1.8462 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4163   -1.2703   -0.2973 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6650   -0.8365    1.3743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3208    1.1505    1.8318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5795    1.7306    0.1577 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7623    1.3679    0.7592 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4875   -0.3454    1.1342 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1265   -0.9482   -1.0955 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0966    0.7541   -1.7037 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0701   -1.0626    0.4839 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  2  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  8 16  1  0
M  END
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PDB for #<Metabolite:0x0000556b6ab28c18>

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      24.094 -15.900   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      25.427 -15.130   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      26.761 -15.900   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      28.095 -15.130   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      29.428 -15.900   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      22.760 -15.130   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      28.095 -13.590   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      22.760 -13.590   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    7                                                  
CONECT    5    4                                                            
CONECT    6    1    8                                                       
CONECT    7    4                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for #<Metabolite:0x0000556b6ab28c18>

COMPND    HMDB0012233
HETATM    1  O1  UNL     1      -2.555  -0.585  -0.578  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.233  -0.275   0.555  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.286   0.830   0.746  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.147   0.492   0.472  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.410   0.017  -0.938  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.844  -0.268  -1.055  1.00  0.00           C  
HETATM    7  O2  UNL     1       2.533   0.409  -1.846  1.00  0.00           O  
HETATM    8  O3  UNL     1       2.416  -1.270  -0.297  1.00  0.00           O  
HETATM    9  H1  UNL     1      -2.665  -0.836   1.374  1.00  0.00           H  
HETATM   10  H2  UNL     1      -1.321   1.150   1.832  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.580   1.731   0.158  1.00  0.00           H  
HETATM   12  H4  UNL     1       0.762   1.368   0.759  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.487  -0.345   1.134  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.126  -0.948  -1.095  1.00  0.00           H  
HETATM   15  H7  UNL     1       0.097   0.754  -1.704  1.00  0.00           H  
HETATM   16  H8  UNL     1       3.070  -1.063   0.484  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    9
CONECT    3    4   10   11
CONECT    4    5   12   13
CONECT    5    6   14   15
CONECT    6    7    7    8
CONECT    8   16
END
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SMILES for #<Metabolite:0x0000556b6ab28c18>

OC(=O)CCCC=O
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INCHI for #<Metabolite:0x0000556b6ab28c18>

InChI=1S/C5H8O3/c6-4-2-1-3-5(7)8/h4H,1-3H2,(H,7,8)
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Synonyms
ValueSource
2-Formylethylacetic acidChEBI
4-Formylbutyric acidChEBI
5-oxo-ValeriansaeureChEBI
5-oxo-Valeric acidChEBI
5-OxopentanoateChEBI
5-Oxovaleric acidChEBI
2-FormylethylacetateGenerator
4-FormylbutyrateGenerator
5-oxo-ValerateGenerator
5-Oxopentanoic acidGenerator
5-OxovalerateGenerator
Glutaric acid semialdehydeGenerator
5-oxo-PentanoateHMDB, Generator
5-oxo-Pentanoic acidHMDB
Glutarate semialdehydeChEBI
Molecular FormulaC5H8O3
Average Mass116.1152
Monoisotopic Mass116.047344122
IUPAC Name5-oxopentanoic acid
Traditional Name5-oxopentanoic acid
CAS Registry Number5746-02-1
SMILES
OC(=O)CCCC=O
InChI Identifier
InChI=1S/C5H8O3/c6-4-2-1-3-5(7)8/h4H,1-3H2,(H,7,8)
InChI KeyVBKPPDYGFUZOAJ-UHFFFAOYSA-N